Table S3. Eukaryotic genomes surveyed in this study Genome
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1 1 2 Table S3. Eukaryotic genomes surveyed in this study Genome Taxonomy Info Sourcea Reference Ascomycota; Sodariomycetes Basidiomycota; Agaricomycotina Blastocladiomycota JGI JGIb JGI Morin et al., 2013 Broad Broad Institutec Ascomycota; Saccharomycotina; Saccharomycetales insertae serdis Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Eurotiomycetes JGI JGIb NCBI Dietrich et al., 2004 Broad Ascomycota; Eurotiomycetes Ascomycota; Dothideomycetes Chytridiomycota NCBI Nierman et al., 2005; Broad Instituted Galagan et al., 2005 JGI JGIb Broad Broad Institutee NCBI Broad Institutef NCBI Jones et al., 2004 NCBI Dujon et al., 2004 JGI JGI JGIb JGIb Broad Broad Instituteg JGI Ohm et al., 2012 Fungi Acremonium alcalophilum Agaricus bisporus Allomyces macrogynus Ascoidea rubescens Ashbya gossypii Aspergillus fumigatus Aspergillus nidulans Aureobasidium pullulans Batrachochytrium dendrobatidis Botryotinia fuckeliana Ascomycota; Leotiomycetes Candida albicans Ascomycota; Saccharomycotina; mitosporic Saccharomycetales Candida glabrata Ascomycota; Saccharomycotina; Saccharomycetaceae Catenaria anguillulae Blastocladiomycota Cladonia grayi Ascomycota; Lecanoromycetes Coccidioides immitis Ascomycota; Eurotiomycetes Cochliobolus Ascomycota; heterostrophus Dothideomycetes 2 Coemansia reversa Conidiobolus coronatus Coprinopsis cinerea Cryphonectria parasitica Cryptococcus neoformans Dacryopinax sp. Debaryomyces hansenii Dekkera bruxellensis Encephalitozoon cuniculi Gibberella zeae Gonapodya prolifera Hanseniaspora valbyensis Hansenula polymorpha Hysterium pulicare Kluyveromyces lactis Kluyveromyces waltii Laccaria bicolor Lipomyces starkeyi Zygomycota; Kickxellomycotina Zygomycota; Entomophthoromycotina Basidiomycota; Agaricomycotina Ascomycota; Sordariomycetes Basidiomycota; Agaricomycotina Basidiomycota; Agaricomycotina Ascomycota; Saccharomycotina; Debaryomycetaceae Ascomycota; Saccharomycotina; Saccharomycetaceae Microsporidia JGI JGIb JGI JGIb Broad Broad Instituteh JGI JGIb Broad Broad Institutei JGI Floudas et al., 2012 NCBI Dujon et al., 2004 JGI Piškur et al., 2012 NCBI Katinka et al., 2001 Ascomycota; Sordariomycetes Chytridiomycota Ascomyocta; Saccharomycotina; Saccharomycetaceae Ascomycota; Saccharomycotina; Saccharomycetales insertae serdis Ascomycota; Dothideomycetes Ascomycota; Saccharomycotina; Sacccharomycetaceae Ascomycota; Saccharomycotina; Saccharomycetaceae Basidiomycota; Agaricomycotina Ascomycota; Saccharomycotina; Lipomycetaceae NCBI Broad Institutej JGI JGI JGIb JGIb JGI JGIb JGI Ohm et al., 2012 NCBI Dujon et al., 2004 JGI Manollis et al., 2004 NCBI Martin et al., 2008 JGI JGIb 3 Lodderomyces elongisporus Magnaporthe oryzae Malassezia globosa Metschnikowia bicuspidata Mixia osmundae Mucor circinelloides Myceliophthora thermophila Mycosphaerella graminicola Neurospora crassa Pachysolen tannophilus Penicillium chrysogenum Phaenerochaete chrysosporium Phaeosphaeria nodorum Phycomyces blakesleeanus Pichia membranifaciens Pichia pastoris Pichia stipitis Piromyces sp. Puccinia graminis Ascomycota; Saccharomycotina; Debaryomycetaceae Ascomycota; Sordariomycetes Basidiomycota; Ustilaginomycotina Ascomycota; Saccharomycotina; Metschnikowiaceae Basidiomycota; Pucciniomycotina Zygomycota; Mucormycotina Ascomycota; Sordariomycetes Ascomycota; Dothideomycetes Broad Broad Institutek Broad Broad Institutel JGI JGIb JGI JGIb JGI Toome et al., 2013 JGI JGIb JGI Berka et al., 2011 JGI Ascomycota; Sordariomycetes Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Eurotiomycetes Basidiomycota; Agaricomycotina Ascomycota; Dothideomycetes Zygomycota; Mucormycotina Ascomycota; Saccharomycotina; Pichiaceae Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Saccharomycotina; Debaryomycetaceae Neocallimastigomycota Basidiomycota; Pucciniomycotina JGI Goodwin et al., 2011; Ohm et al., 2012 Galagan et al., 2003 JGI JGIb NCBI JGI van den Berg et al., 2008 Martinez et al., 2004 Broad Broad Institutem JGI JGIb JGI JGIb NCBI De Schutter et al., 2009 JGI Jeffries et al., 2007 JGI Broad JGIb Broad Instituten 4 Rhizophagus irregularis Rhizopus oryzae Rhodotorula graminis Rhytidhysteron rufulum Rozella allomycis Saccharomyces bayanus Saccharomyces castellii Saccharomyces cerevisiae Saccharomyces kluyveri Saccharomyces mikatae Saccharomyces paradoxus Saitoella complicata Schizophyllum commune Schizosaccharomyces pombe Sclerotinia sclerotiorum Spathaspora passalidarum Sphaerobolus stellatus Spizellomyces punctatus Thielavia terrestris Glomeromycota JGI JGIb Zygomycota; Mucormycotina Basidiomycota; Pucciniomycotina Ascomycota; Dothideomycetes Cryptomycota Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Taphrinomycotina Basidiomycota; Agaricomycotina Ascomycota; Taphrinomycotina Ascomycota; Leotiomycetes Ascomycota; Saccharomycotina; Debaryomycetaceae Basidiomycota; Agaricomycotina Chytridiomycota Broad Ma et al., 2009 JGI JGIb JGI Ohm et al., 2012 JGI SGD James et al., 2013 Kellis et al., 2003 SGD Cliften et al., 2003 SGD SGD Goffeau et al., 1996; Cherry et al., 1997; Liti et al., 2009 The Genolevures Consortium et al., 2009 Kellis et al., 2003 SGD Kellis et al., 2003 JGI JGIb JGI Ohm et al., 2010 Broad Broad Instituteo Broad Broad Institutep JGI Wohlbach et al., 2011 JGI JGIb JGI Broad Institutec Ascomycota; Sordariomycetes JGI Berka et al., 2011 SGD 5 Tremella mesenterica Basidiomycota; Agaricomycotina Ascomycota; Sordariomycetes Ascomycota; Pezizomycetes Basidiomycota; Ustilaginomycotina Ascomycota; Saccharomycotina; Saccharomycetaceae Ascomycota; Saccharomycotina; Phaffomycetaceae Ascomycota; Lecanoromycetes Ascomycota; Xylonomycetes Ascomycota; Saccharomycotina; Dipodascaceae Ascomycota; Saccharomycotina; Saccharomycetaceae JGI Floudas et al., 2012 JGI Martinez et al., 2008 JGI Martin et al., 2010 Broad Kämper et al., 2006 JGI Scannell et al., 2007 JGI JGIb JGI JGIb JGI JGIb NCBI Dujon et al., 2004 JGI The Genolevures Consortium et al., 2009 Caenorhabditis elegans Metazoa, Nematoda WormBase Canis familiaris Metazoa, Chordata, Craniata NCBI C. elegans Sequencing Consortium, 1998 Lindblad-Toh et al., 2005 Capsaspora owczarzaki Danio rerio Fungi/Metazoa insertae serdis, Filasterea Metazoa, Chordata, Craniata Metazoa, Arthopoda Broad Broad Institutec NCBI Howe et al., 2013 NCBI Adams et al., 2000 Metazoa, Chordata, Craniata NCBI International Human Genome Sequencing Consortium, 2001; Venter et al., 2001 Trichoderma reesei Tuber melanosporum Ustilago maydis Vanderwaltozyma polyspora Wickerhamomyces anomalus Xanthoria parietina Xylona heveae Yarrowia lipolytica Zygosaccharomyces rouxii Holozoa Drosophila melanogaster Homo sapiens 6 Monosiga brevicollis Mus musculus Nematostella vectensis Salpingoeca rosetta Sphaeroforma arctica Thecamonas trahens Fungi/Metazoa insertae sedis, Choanoflagellida Metazoa, Chordata, Craniata JGI King et al., 2008; Broad Institutec NCBI Metazoa, Cnidaria JGI Mouse Genome Sequencing Consortium, 2002 Putnam et al., 2007 Fungi/Metazoa insertae sedis, Choanoflagellida Fungi/Metazoa insertae sedis, Ichthyosporea Apusomonadidae Broad Broad Institutec Broad Broad Institutec Broad Broad Institutec BCM-HGSC Clarke et al., 2013 dictyBase Eichinger et al., 2005 Loftus et al., 2005 Amoebozoa Acanthamoeba Acanthamoebae castellanii Dictyostelium Dictyostelids discoideum Entamoeba histolytica Archamoebae, Entamoebae AmoebaDB Archaeplastida Arabidopsis thaliana Chlamydomonas reinhardtii Cyanidioschyzon merolae Micromonas sp. Oryza sativa Viridiplantae, Streptophyta, Embryophytes Viridiplantae, Chlorophyta, Chlorophyceae, Chlamydomonadales Rhodoplastids, Cyanidiophytes Viridiplantae, Chlorophyta, Mamiellales Viridiplantae, Streptophyta, Embryophytes NCBI Phytozome Arabidopsis Genome Initiative, 2000 Merchant et al., 2007 C. merolae genome project JGI Matsuzaki et al., 2004 NCBI Goff et al., 2002 Worden et al., 2009 7 Ostreococcus tauri Populus trichocarpa Volvox carteri Viridiplantae, Chlorophyta, Mamiellales Viridiplantae, Streptophyta, Embryophytes Viridiplantae, Chlorophyta, Chlorophyceae, Chlamydomonadales JGI Palenik et al., 2007 Phytozome Tuskan et al., 2006 Phytozome Prochnik et al., 2010 Rhizaria, Cercoza, Filosa, Chlorarachniophytes Alveolates, Apicomplexa JGI Curtis et al., 2012 CryptoDB Alveolates, Ciliates ORCAE Abrahamsen et al., 2004 Cock et al., 2010 Stramenopiles JGI Tyler et al., 2006 Alveolates, Apicomplexa PlasmoDB Gardner et al., 2002 Alveolates, Ciliates TGD Eisen et al., 2006 Stramenopiles JGI Alveolates, Apicomplexa Alveolates, Apicomplexa NCBI ToxoDB Armbrust et al., 2004 Gardner et al., 2005 Kissinger et al., 2003 Haptophytes Cryptophytes JGI JGI Read et al., 2013 Curtis et al., 2012 Discoba, Euglenozoa, Kinetoplastida, Bodonidae - In preparationq SAR Bigelowiella natans Cryptosporidium parvum Ectocarpus siliculosus Phytophthora ramourum Plasmodium falciparum Tetrahymena thermophila Thalassiosira pseudonana Theileria parva Toxoplasma gondii CCTH Emiliania huxleyi Guillardia theta Excavata Bodo saltans 8 Crithidia fasciculata Giardia sp. Leishmania major Naegleria gruberi Trichomonas vaginalis Trypanosoma brucei Trypanosoma cruzi 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 a Discoba, Euglenozoa, Kinetoplastida, Trypanosomatidae Fornicata, Diplomonadida Discoba, Euglenozoa, Kinetoplastida, Trypanosomatidae Discoba, Heterolobosea Metamonads, Parabasalia TriTrypDB Aslett et al., 2009 GiardiaDB Aurrecoechea et al., 2009 Ivens et al., 2005 Discoba, Euglenozoa, Kinetoplastida, Trypanosomatidae Discoba, Euglenozoa, Kinetoplastida, Trypanosomatidae TriTrypDB Berriman et al., 2005 TriTrypDB El-Sayed et al., 2005 TriTrypDB JGI TrichDB Fritz-Laylin et al., 2010 Carlton et al., 2007 SGD (yeastgenome.org); NCBI (nchi.nlm.nih.gov); JGI (genome.jgi.doe.gov/programs/fungi/index.jsf); Broad Institute (broadinstitute.org); WormBase (wormbase.org); BCM-HGSC (hgsc.bcm.edu/microbiome/acanthamoeba-castellanineff); dictyBase (dictybase.org); AmoebaDB (amoebadb.org); Phytozome (phytozome.net); C. merolae genome project (merolae.biol.s.u-tokyo.ac.jp); CryptoDB (cryptodb.org); ORCAE (bioinformatics.psb.ugent.be/orcae/overview/Ectsi); PlasmoDB (plasmodb.org); TGD (ciliate.org); ToxoDB (toxodb.org); GiardiaDB (giardiadb.org); TriTrypDB (tritrypdb.org) b Unpublished sequence data produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) in collaboration with the user community. c The Origins of Multicellularity Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). d Aspergillus Comparative Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). e The Batrachochytrium dendrobatidis Genome Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). f The Botrytis cinerea Genome Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). g Coccidioides group Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). h Coprinopsis cinerea Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). i Cryptococcus neoformans var. grubii H99 Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). 9 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 j The Fusarium Comparative Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). k Candida Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). l Magnaporthe comparative Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). m Stagonospora nodorum Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). n Puccinia Group Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). o Schizosaccharomyces group Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). p Sclerotinia sclerotiorum Sequencing Project, Broad Institute of Harvard and MIT (broadinstitute.org). q Unpublished data (Andrew Jackson, University of Liverpool). 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